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- PDB-2ztd: MtRuvA Form III -

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Basic information

Entry
Database: PDB / ID: 2ztd
TitleMtRuvA Form III
ComponentsHolliday junction ATP-dependent DNA helicase ruvA
KeywordsDNA BINDING PROTEIN / RECOMBINATION / branch migration / Holliday junction / DNA binding / oligomerization / acidic pin / ATP-binding / DNA damage / DNA recombination / DNA repair / DNA-binding / Helicase / Hydrolase / Nucleotide-binding / SOS response
Function / homology
Function and homology information


Holliday junction helicase complex / Holliday junction resolvase complex / four-way junction helicase activity / SOS response / four-way junction DNA binding / double-strand break repair via homologous recombination / DNA helicase / DNA recombination / DNA repair / DNA damage response ...Holliday junction helicase complex / Holliday junction resolvase complex / four-way junction helicase activity / SOS response / four-way junction DNA binding / double-strand break repair via homologous recombination / DNA helicase / DNA recombination / DNA repair / DNA damage response / ATP hydrolysis activity / DNA binding / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
Bacterial DNA recombination protein RuvA / Holliday junction DNA helicase RuvA, C-terminal / DNA helicase, Holliday junction RuvA type, domain I, bacterial / RuvA, C-terminal domain superfamily / RuvA N terminal domain / RuvA, C-terminal domain / Ubiquitin-associated (UBA) domain / RuvA domain 2-like / Helix-hairpin-helix domain / Helix-hairpin-helix DNA-binding motif, class 1 ...Bacterial DNA recombination protein RuvA / Holliday junction DNA helicase RuvA, C-terminal / DNA helicase, Holliday junction RuvA type, domain I, bacterial / RuvA, C-terminal domain superfamily / RuvA N terminal domain / RuvA, C-terminal domain / Ubiquitin-associated (UBA) domain / RuvA domain 2-like / Helix-hairpin-helix domain / Helix-hairpin-helix DNA-binding motif, class 1 / Helix-hairpin-helix DNA-binding motif class 1 / Helicase, Ruva Protein; domain 3 / Nucleic acid-binding proteins / 5' to 3' exonuclease, C-terminal subdomain / DNA polymerase; domain 1 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Holliday junction ATP-dependent DNA helicase RuvA / Holliday junction branch migration complex subunit RuvA
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsPrabu, J.R. / Thamotharan, S. / Khanduja, J.S. / Chandra, N.R. / Muniyappa, K. / Vijayan, M.
CitationJournal: Biochim.Biophys.Acta / Year: 2009
Title: Crystallographic and modelling studies on Mycobacterium tuberculosis RuvA Additional role of RuvB-binding domain and inter species variability
Authors: Prabu, J.R. / Thamotharan, S. / Khanduja, J.S. / Chandra, N.R. / Muniyappa, K. / Vijayan, M.
History
DepositionOct 1, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 5, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Holliday junction ATP-dependent DNA helicase ruvA
B: Holliday junction ATP-dependent DNA helicase ruvA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1096
Polymers43,7402
Non-polymers3684
Water2,036113
1
A: Holliday junction ATP-dependent DNA helicase ruvA
B: Holliday junction ATP-dependent DNA helicase ruvA
hetero molecules

A: Holliday junction ATP-dependent DNA helicase ruvA
B: Holliday junction ATP-dependent DNA helicase ruvA
hetero molecules

A: Holliday junction ATP-dependent DNA helicase ruvA
B: Holliday junction ATP-dependent DNA helicase ruvA
hetero molecules

A: Holliday junction ATP-dependent DNA helicase ruvA
B: Holliday junction ATP-dependent DNA helicase ruvA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,43424
Polymers174,9618
Non-polymers1,47416
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area25600 Å2
ΔGint-187.4 kcal/mol
Surface area61720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.670, 94.830, 99.210
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11B-511-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A 1-131, 147-194
211chain B 1-131, 147-194

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Components

#1: Protein Holliday junction ATP-dependent DNA helicase ruvA


Mass: 21870.078 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: ruvA / Plasmid: pMTRA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: P66744, UniProt: P9WGW3*PLUS, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.41 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Crystallized in the presence of equimolar Holliday Junction using 0.1M sodium succinate, pH5.0, 1.4M ammonium sulfate, pH8.0, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 4, 2007 / Details: Mirrors
RadiationMonochromator: OSMIC MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 15211 / % possible obs: 92.4 % / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Biso Wilson estimate: 29.66 Å2 / Rmerge(I) obs: 0.103 / Net I/σ(I): 7.7
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.454 / Mean I/σ(I) obs: 1.9 / Num. unique all: 2307 / % possible all: 96.7

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Processing

Software
NameClassification
PHENIXrefinement
MAR345dtbdata collection
MOSFLMdata reduction
SCALAdata scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2H5X

2h5x


Resolution: 2.4→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.268 1054 6.93 %RANDOM
Rwork0.2043 ---
obs0.2043 15210 --
Displacement parametersBiso mean: 37.46 Å2
Baniso -1Baniso -2Baniso -3
1-4.3932 Å20 Å20 Å2
2---3.0406 Å20 Å2
3----1.3526 Å2
Refinement stepCycle: LAST / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2675 0 24 113 2812
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.008
X-RAY DIFFRACTIONf_dihedral_angle_d13.897
X-RAY DIFFRACTIONf_angle_d1.108
X-RAY DIFFRACTIONf_improper_angle_d0.8
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1316X-RAY DIFFRACTIONPOSITIONAL
12B1316X-RAY DIFFRACTIONPOSITIONAL0.063
LS refinement shellResolution: 2.4→2.5 Å
RfactorNum. reflection% reflection
Rfree0.3327 131 -
Rwork0.2467 --
obs-1834 96 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.53430.1382-0.41290.6323-0.23230.25510.0565-0.218-0.00670.1469-0.1373-0.2536-0.13290.1358-0.16050.0097-0.0080.07360.0219-0.0334-0.0148-25.70642.352613.861
20.05860.00390.01120.0190.00920.04480.1702-0.07480.21740.0414-0.17560.0775-0.14370.174400.1822-0.09090.05820.2108-0.0360.1885-11.504315.500723.2457
30.02460.0101-0.01270.03950.0136-0.00020.12780.02630.28320.0161-0.2320.07670.04730.2134-0.00060.2290.01650.08850.1308-0.03330.1796-19.716836.14870.1763
40.0593-0.07370.03730.1565-0.05170.30980.052-0.02850.0101-0.2690.0773-0.02760.0799-0.24630.1473-0.15770.2348-0.0698-0.16510.03880.084-18.651433.59847.2804
50.09650.03070.0130.03870.00050.05840.16110.3469-0.3758-0.2080.09570.0187-0.0571-0.03470.00080.10310.0343-0.05670.2248-0.04310.1853-32.869724.345134.0562
60.0025-0.0442-0.01810.03140.00850.04360.02660.1562-0.1208-0.03680.08390.06810.05990.0972-0.00010.26180.04490.04870.2266-0.04870.141-24.736347.818713.4515
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A 1-63
2X-RAY DIFFRACTION2chain A 65-131
3X-RAY DIFFRACTION3chain A 147-194
4X-RAY DIFFRACTION4chain B 1-63
5X-RAY DIFFRACTION5chain B 65-131
6X-RAY DIFFRACTION6chain B 147-194

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